Hi, The best way to get started with marvin is to build off the eginput example.
Stuff you'll need to assemble: 1. a PSF file for your protein, of course. 2. a shift table for your protein. 3. a NOESY peak location table for your protein. Regarding the shift table, it doesn't have to be in PIPP format. I can also read NMR-STAR, although you have to be careful to get the degeneracy codes correct. If you want to read NMR-STAR shift tables, add the line "package require nmrstar" to the top of the initMatch* scripts. Then change the call to readPippShiftTable to readNmrStarShiftTable. In the call to createShiftAssignments, you can set the various selections to exclude atoms that aren't observable in your particular spectrum (eg., backbone amides, if your 3dC was collected in D2O). Regarding the NOESY peak location table, it also doesn't have to be in PIPP format. I can read Xeasy and nmrDraw's formats as well. If you want to use one of those formats, add a "package require xeasy" or "package require nmrdraw" line to the top, and change the call to process3dCPippPeakTable to process3dCXeasyPeakTable or process3dCNmrDrawPeakTable. You'll have to identify each column in the peak table, using the flags to your process*PeakTable call, as illustrated in the CVN example. Then you'll have to set the peak folding/aliasing flags to match your spectrum. These flags are repeated for each call to match3d. The relevant ones are -nonFoldedPeaksArePositive or -nonFoldedPeaksAreNegative -signChangesUponFoldingFromHeavyatomDimension -signChangesUponFoldingFromProtonDimension -signChangesUponFoldingToProtonDimension -shiftsAliasedAlongFromHeavyatomDimension or - shiftsFoldedAlongFromHeavyatomDimension -shiftsAliasedAlongFromProtonDimension or - shiftsFoldedAlongFromProtonDimension -shiftsAliasedAlongToProtonDimension or - shiftsFoldedAlongToProtonDimension The meaning of these flags should be obvious. The last three flags are a bit more complex: -fromProtonSpectralRangePPM [list -1.1 9.5] -fromHeavyatomSpectralRangePPM [list 60 120] -toProtonSpectralRangePPM [list -1.2 6.0] (The numbers in the above lines are just examples. ) The list of two numbers after each flag define the chemical shifts around which the actual aliasings/foldings take place. For now, getting them right is left in your hands, unless you're using PIPP peak location tables, which include the necessary information in their headers. I'm working with Frank Delaglio to see if we can build something general-purpose that could read that information out of nmrPipe spectra, but it's not there yet. If you don't get the spectral range flag values correct, marvin will have a difficult time assigning peaks with folded/aliased positions. You'll need to change the names of the output .peaks, .shiftAssignments, and .exceptions files to something you like. And if you have a reference structure, replace the name of cvn_reference.pdb with the name of the PDB file for your reference structure. If you don't have one (as is usually the case, of course), just delete those lines. Finally, you'll need to update the sa_pass* and summarize_pass* files. The necessary changes are all just filename changes, which should be obvious. I'm sure you'll run into more questions as you continue. Ask away. --JK On Jun 11, 2007, at 6:19 PM, gary thompson wrote: > some questions about marvin > > where should I start? do i need to alter much other than > > 1. alters the input peak and shifts lists psf files and file name > roots > 2. remove opening of reference pdb files e.g . delete > > readPDB -fileName ./cvn_reference.pdb > > and > > initialShiftAssignmentAnalysis \ > -pot $noe \ > -referenceStructureFile ./cvn_reference.pdb \ > -minLikelihood 0.9 \ > > etc... > > > also > is there any more documentation on whats going on other than the > source code, paper, slides on th web and the cvn example? > > > regards and many thanks > gary > > n.b. what sort of hardware were the timings you reported (60 > processors 12 hours) made on? > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
